From: Anna James (annajamesmatrix_at_hotmail.com)
Date: Tue Aug 16 2011 - 09:20:49 CDT
I understood your point but I use the following script on my solvent.pdb generated using packmol to get the psf out of it.
package require psfgen
topology topology27.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment QQQ {pdb solvent.pdb}
coordpdb solvent.pdb QQQ
guesscoord
writepdb solvent.pdb
writepsf solvent.psf
How do I generate psf file that could accomodate multiple segments? .Please suggest me changes in the above script.
I could do with two more segments giving me 9999*2 extra residues (naming TTT and RRR) and I could possibly make required changes in the solvation script to consider the two more SEGIds
In anticipation of an encouraging reply
Anna James Vaughan
Leeds
> Date: Tue, 16 Aug 2011 09:43:00 -0400
> Subject: Re: namd-l:
> From: akohlmey_at_gmail.com
> To: annajamesmatrix_at_hotmail.com
> CC: namd-l_at_ks.uiuc.edu
>
> On Tue, Aug 16, 2011 at 9:38 AM, Anna James <annajamesmatrix_at_hotmail.com> wrote:
> > Hello NAMD Experts
> >
> >
> > I have a query about setting up a PBC unit.Unfortunately I am working with a
> > large Globular Protein,the extent of which is around 90A in all the three
> > X,Y Z axes that would mean My PBC Unit has to be larger than it to encompass
> > the whole protein. I Created a Methanol Box of 100*100*100 A and filled it
> > up with Methanol molecules as the per the density of Methanol .The number of
> > Molecules exceeded 35000 and VMD/PSFGEN cannot process PDBs that have
> > residues more than 9999.
>
> just use multiple segments (and multiple files). the numbers
> can start fresh for each segment.
>
> axel.
>
> >
> > I am sure lot of people would have worked with PBC units as large as 90A
> > ,What is the way to go about solvating them ?Do we have to compromise on the
> > number of Methanol Molecules while setting up the system?
> >
> > I am using the following parameters :
> >
> > exclude scaled1-4
> > 1-4scaling 1.0
> > cutoff 12.0
> > switching on
> > switchdist 10.0
> > pairlistdist 14.0
> > timestep 2.0
> > rigidBonds all
> > nonbondedFreq 1 .
> >
> > Looking at the above parameters, What would be the safe distance between the
> > images while setting up PBC units?
> > Are the above parameters good enough ?
> >
> >
> > In anticipation of an encouraging reply
> >
> >
> > Anna James Vaughan
> > Leeds
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
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